In this paper, we develop a new method based on ultra-low-energy ion implantation through a stencil mask to locally fabricate Si nanocrystals in an ultrathin silica layer. We perform a 1 keV Si implantation with doses of 5×1015 Si+/cm2, 7.5×1015 Si+/cm2 and 1×1016 Si+/cm2 in a 7 nm thick silicon oxide layer through stencil mask apertures ranging from 1μm up to 5 μm. After the mask removal the samples are furnace annealed at a temperature of 1050°C for 90 min under N2 atmosphere. The samples are then characterized by mapping the implanted and non-implanted areas by atomic force microscopy and photoluminescence spectroscopy. The intensity and the wavelength of the PL peak are found to depend on the implanted NCs cell size. A slight blue shift from 730 nm up to 720 nm is observed with decreasing cell size. Simultaneously, the PL intensity decreases and the signal vanishes for submicron features (which should contain 102 to 103 NCs). AFM microcopy performed on the implanted regions shows that the well-known oxide swelling usually observed after NCs synthesis decreases from 3.5 nm down to 0 as the cell size decreases. This result demonstrates that the effective implanted dose clearly decreases with the size of the cells. This effect is probably due to an electrostatic charging of the Si3N4 membrane despite the metallization treatments applied to the mask surface.